Summarize a tpmatrix object storing transition probability matrices.
Summary statistics are computed for each possible transition.
# S3 method for tpmatrix
summary(object, id = NULL, probs = NULL, unflatten = FALSE, ...)A tpmatrix object.
A tpmatrix_id object for which columns contain the ID variables
for each row in object. If not NULL, then transition probability matrices
are summarized by the ID variables in id.
A numeric vector of probabilities with values in [0,1] used
to compute quantiles. Computing quantiles can be slow when object is large,
so the default is NULL, meaning that no quantiles are computed.
If FALSE, then each column containing a summary statistic
is a vector and the generated table contains one row
(for each set of ID variables) for each possible transition; if
TRUE, then each column stores a list of matrix objects containing
transition probability matrices formed by "unflattening" the one-dimensional
vectors. See "Value" below for additional details.
Additional arguments affecting the summary. Currently unused.
If unflatten = "FALSE" (the default), then a data.table
is returned with columns for (i) the health state that is being transitioned
from (from), (ii) the health state that is being transitioned to (to)
(iii) the mean of each parameter across parameter samples (mean),
(iv) the standard deviation of the parameter samples (sd), and
(v) quantiles of the parameter samples corresponding to the probs argument.
If, on the other hand, unflatten = "TRUE", then the parameters are unflattened
to form transition probability matrices; that is, the mean, sd, and
quantile columns are (lists of) matrices.
In both cases, if id is not NULL, then the ID variables are also
returned as columns.
library("data.table")
hesim_dat <- hesim_data(strategies = data.table(strategy_id = 1:2),
patients = data.table(patient_id = 1:3))
input_data <- expand(hesim_dat, by = c("strategies", "patients"))
# Summarize across all rows in "input_data"
p_12 <- ifelse(input_data$strategy_id == 1, .8, .6)
p <- tpmatrix(
C, p_12,
0, 1
)
## Summary where each column is a vector
summary(p)
#> from to mean sd
#> <char> <char> <num> <num>
#> 1: s1 s1 0.3 0.1095445
#> 2: s1 s2 0.7 0.1095445
#> 3: s2 s1 0.0 0.0000000
#> 4: s2 s2 1.0 0.0000000
summary(p, probs = c(.025, .975))
#> from to mean sd 2.5% 97.5%
#> <char> <char> <num> <num> <num> <num>
#> 1: s1 s1 0.3 0.1095445 0.2 0.4
#> 2: s1 s2 0.7 0.1095445 0.6 0.8
#> 3: s2 s1 0.0 0.0000000 0.0 0.0
#> 4: s2 s2 1.0 0.0000000 1.0 1.0
## Summary where each column is a matrix
ps <- summary(p, probs = .5, unflatten = TRUE)
ps
#> mean sd 50%
#> <list> <list> <list>
#> 1: 0.3,0.0,0.7,1.0 0.1095445,0.0000000,0.1095445,0.0000000 0.3,0.0,0.7,1.0
ps$mean
#> [[1]]
#> s1 s2
#> s1 0.3 0.7
#> s2 0.0 1.0
#>
# Summarize by ID variables
tpmat_id <- tpmatrix_id(input_data, n_samples = 2)
p_12 <- ifelse(tpmat_id$strategy_id == 1, .8, .6)
p <- tpmatrix(
C, p_12,
0, 1
)
## Summary where each column is a vector
summary(p, id = tpmat_id)
#> strategy_id patient_id from to mean sd
#> <int> <int> <char> <char> <num> <num>
#> 1: 1 1 s1 s1 0.2 0
#> 2: 1 1 s1 s2 0.8 0
#> 3: 1 1 s2 s1 0.0 0
#> 4: 1 1 s2 s2 1.0 0
#> 5: 1 2 s1 s1 0.2 0
#> 6: 1 2 s1 s2 0.8 0
#> 7: 1 2 s2 s1 0.0 0
#> 8: 1 2 s2 s2 1.0 0
#> 9: 1 3 s1 s1 0.2 0
#> 10: 1 3 s1 s2 0.8 0
#> 11: 1 3 s2 s1 0.0 0
#> 12: 1 3 s2 s2 1.0 0
#> 13: 2 1 s1 s1 0.4 0
#> 14: 2 1 s1 s2 0.6 0
#> 15: 2 1 s2 s1 0.0 0
#> 16: 2 1 s2 s2 1.0 0
#> 17: 2 2 s1 s1 0.4 0
#> 18: 2 2 s1 s2 0.6 0
#> 19: 2 2 s2 s1 0.0 0
#> 20: 2 2 s2 s2 1.0 0
#> 21: 2 3 s1 s1 0.4 0
#> 22: 2 3 s1 s2 0.6 0
#> 23: 2 3 s2 s1 0.0 0
#> 24: 2 3 s2 s2 1.0 0
#> strategy_id patient_id from to mean sd
## Summary where each column is a matrix
ps <- summary(p, id = tpmat_id, unflatten = TRUE)
ps
#> strategy_id patient_id mean sd
#> <int> <int> <list> <list>
#> 1: 1 1 0.2,0.0,0.8,1.0 0,0,0,0
#> 2: 1 2 0.2,0.0,0.8,1.0 0,0,0,0
#> 3: 1 3 0.2,0.0,0.8,1.0 0,0,0,0
#> 4: 2 1 0.4,0.0,0.6,1.0 0,0,0,0
#> 5: 2 2 0.4,0.0,0.6,1.0 0,0,0,0
#> 6: 2 3 0.4,0.0,0.6,1.0 0,0,0,0
ps$mean
#> [[1]]
#> s1 s2
#> s1 0.2 0.8
#> s2 0.0 1.0
#>
#> [[2]]
#> s1 s2
#> s1 0.2 0.8
#> s2 0.0 1.0
#>
#> [[3]]
#> s1 s2
#> s1 0.2 0.8
#> s2 0.0 1.0
#>
#> [[4]]
#> s1 s2
#> s1 0.4 0.6
#> s2 0.0 1.0
#>
#> [[5]]
#> s1 s2
#> s1 0.4 0.6
#> s2 0.0 1.0
#>
#> [[6]]
#> s1 s2
#> s1 0.4 0.6
#> s2 0.0 1.0
#>